KABUL: Taliban leader Mullah Omar warned Sunday an agreement between Washington and Kabul on maintaining a US military presence in Afghanistan after 2014 would have "serious consequences".

The United States and Afghanistan are negotiating the Bilateral Security Agreement (BSA) on the future of US forces in Afghanistan when NATO's mission ends in late 2014, including the number of bases and the status of any soldiers remaining there.

After marathon talks in Kabul, Afghan President Hamid Karzai and US Secretary of State John Kerry announced Saturday that they had reached a partial agreement, but had been unable to fully resolve the sensitive issue of American troop immunity.

"The invaders and their allies should understand (the signature) of the strategic agreement would have serious consequences for them," Mullah Omar said in a statement posted on a Taliban website.

The rebel leader also warned the US the maintenance of its bases on Afghan soil "will never be accepted" and "armed jihad will continue against them with more momentum."

The signing of a security agreement with the Americans would give the Afghan army, which is under-equipped and plagued by desertion, a supporting force after the withdrawal of 87,000 NATO troops by the end of 2014.

Despite the sticking point of troop immunity, US officials were upbeat about the progress of the BSA security deal negotiations on Sunday, as Kerry left Kabul for London.

"From our vantage, (the visit was) positive in that we reached a basic agreement on all the key issues," a senior US official told reporters.

The departure of coalition troops will take place against a sensitive political backdrop, with Afghanistan's presidential elections scheduled for April 5.

In his statement, Mullah Omar reiterated that he "rejected" the elections, which he said were being manipulated by foreign powers, and called on Afghans not to participate.

The hardline Taliban regime was driven from power by a US-led coalition in 2001 for sheltering the Al-Qaeda leaders behind the 9/11 attacks. (AFP)